Sunday, September 18, 2016

Ancestral North & South Indians and South Asia

A while back, actually almost 8 years ago, Dr. David Reich at Harvard Med and his colleagues came out with a rather intriguing model for South Asian population genetics. They proposed that virtually all South Asians were mostly some sort of mixture between two core populations. Ancestral North Indians and Ancestral South Indians with the model only growing more complex ever since. [1]



South Asia


The basic concept being that one population related to modern-day West Asians and Europeans came in from the Northwest (ANIs) whilst one was seemingly indigenous to South Asia and was, originally, proposed to be somewhat intermediary between West Eurasians and East Asians (ASIs). 


And, as you can see, the model got somewhat more complex as time went by, even without our recent influxes of ancient DNA. "ANI" came to be seen for what it was; a composite. It seems to be mostly made up of Neolithic Iranian-related ancestry with some steppe ancestry owed to Indo-Aryan speaking pastoral nomads whose descendants descended upon Central and South Asia late into the Bronze Age, bringing the Indo-Aryan languages to South Asia. [note]

There they would have encountered farmers of the BMAC culture in Central Asia who were likely quite Neolithic Iranian-like. These Indo-Aryan speakers, likely quite similar to Northeastern Europeans (i.e. Lithuanians), most likely intermixed with farmers in Central Asia and then moved on into Northwestern South Asia (i.e. the Indus Valley) to a pre-modern civilization more or less on the verge of collapsing (The Indus Valley Civilization) and from there; further intermixing with locals seems to have occurred.


IVC on the decline close to when the Indo-Aryan speakers began arriving


In my opinion, based on the population genetics of modern South Asians, the inhabitants of Northwestern South Asia were likely, as is likely the case with the BMAC farmers, quite similar to Neolithic Iranians and were thus a mixture between Basal-rich/"ENF"-like ancestry and Ancient North Eurasian-related ancestry. They probably, at this point in time, also carried ancestry from local Hunter-Gatherers whom they'd encroached upon by migrating over from West Asia and that's where "ASI" comes in.

The local Hunter-Gatherers look to have been Andamanese and Australo-Melanesian-related peoples who today have their most persistent descendants in populations like Paniyas who actually cluster somewhat close to the likes of Papuans on a global PCA (principal component analysis) based on 166,000 autosomal SNPs:



The "ASI" model somewhat changed in that ASI now seems like something Eastern Non-African  (rather than being some intermediate between West Eurasians and East Asians) and is often acknowledged by academics such as Reich to be something related to Andamanese Islanders like the Onge, hence why the Onge are used as a stand-in for "ASI" in this run from the recent Lazaridis et al. paper:
Onges are probably somewhat better stand-ins than Paniyas since they seem to lack West Eurasian admixture entirely when Paniyas, despite looking to be mostly "Eastern Non-African", are definitely partly West Eurasian so something like an ADMIXTURE cluster based on them and some other heavily ASI admixed South Asians won't yield a pristine enough "ASI" stand-in. Though Harappa did a pretty good job as far as I can see.

Granted, even utilizing Onges won't really do as, while they're certainly related to whatever "ASI" is, they're definitely not exactly like it and some notable genetic drift has occurred between the two as far as I can tell. Basically, we need ancient DNA if we're to really make things solid when dealing with ASI

Paniya Man

Things also became a little more complicated on the West Eurasian front lately. For example, you might notice that that figure from the Lazaridis paper shows more "Steppe" related ancestry in the various South Asian populations than the Harppa run implies.

This is mostly because, up until now, we've generally seen the Steppe admixture in South Asians as being something Northeastern European-like (i.e. similar to Lithuanians) based on how South Asians often registered such ancestry alongside Gedrosian, Caucasus (or Caucasus-Gedrosia which seems to correlate well with the Neolithic Iranian and Caucasus Hunter-Gatherher-like ancestry in the region), Southwest Asian and Mediterranean. (some bits of these other clusters like "Mediterranean" are probably owed to their steppe ancestors too) [note]




And lo and behold, when we finally got our hands on some Sintashta and Andronovo cultures samples; they indeed looked quite similar to modern Northeastern Europeans. A mixture between Yamnaya-like people, Neolithic Anatolians and Villabruna-Cluster Hunter-Gatherer (WHG) ancestry leaning more on being Yamnaya-like.

This is important because the Sintashta and Andronovo cultures are pretty much accepted by most to be early Indo-Iranian speaking steppe cultures and as being the source for the Indo-Iranian languages in Iran and South Asia (Iranian languages in West Asia, Afghanistan and Pakistan + Indo-Aryan languages in South Asia). [4]

So... Things should seem settled I suppose and the old "Caucasus-Gedrosia + Mediterranean + Southwest Asian + Northeastern European + Ancestral South Indian + others" model should be all done, no? South Asians are probably, in my humble opinion, something Sintashta-Andronovo-like + something Neolithic Iranian-like + ASI + others. 

But, some argue that the model is just somewhat different and roughly agree with the figure above which implies that the steppe ancestry in South Asia is perhaps more Yamnaya-like [note] and thus, thanks to the greater Caucasus Hunter-Gatherer-related ancestry (Caucasus Hunter-Gatherers and Neolithic Iranians are very closely related) in these types of steppe pastoralists; South Asians (as well as others) might be more Steppic than originally imagined via models dependent on Northeastern Europeans and ancients like Sintashtas. 

David Wesolowski over at Eurogenes is one proponent of this alternative view on things. However, I personally don't, for now, make much of this model. I think Yamnaya-like steppe pastoralists prove a better fit at times because of their Caucasus Hunter-Gatherer-related ancestry which works to deflate the Neolithic Iranian-related ancestry in South Asians and over-represent how "steppe" they really are.

Their steppe ancestry levels, in my humble opinion, are perhaps somewhat decently-represented by the data in an old run created by "Kurd" at Anthrogenica where he used Sintashta samples which was then pored over by the author of Vaedhya to show us the following results:



I find the alternative Yamnaya-like admixture model less convincing because, as far as I know, there's really no archaeological proof for Yamnaya-Afanasevo-like pastoralists making deep incursions into Central Asia and Northwestern South Asia and, even if they did, it's strange that they'd remain so heavily steppe after wading through Central Asia (inhabited by farmers such as those of the BMAC culture who were most likely Neolithic Iranian-like for the most part), Afghanistan and then also more northerly areas of Northwestern South Asia given the heavy steppe proportions that arise when they're utilized on South Asians. [note]

For all I know, David could very well be right here but, for the time being, I find the "Sintasha-Andronovo-like + Neolithic Iranian-like + ASI + others" model more convincing than anything else. 

But regardless of which of the two models is true, most South Asians are mostly made up of Neolithic-Iranian-related ancestry, some form of Steppe ancestry and whatever ASI exactly is, alongside negligible, non-existent, or quite notable admixture from the likes of East Asian-related people and Africans depending on the population (i.e. Bengalis and their notable East/Southeast Asian-related ancestry). 

Things will definitely become more clear once ancient DNA starts flooding in from South Asia and I hear that's certainly in the works. 


References:





Notes:

1. There is interestingly a phenotypic and not just genetic difference between Yamnaya-like people and Sintashta-Andronovo-like people: [-]

2. There is apparently some notable Ancient North Eurasian-related ancestry in South Indian populations like Paniyas despite how they don't at all show more proper "West Eurasian" components to justify the levels of ANE-related ancestry they show. i.e. I've heard but can't confirm that groups like Paniyas may show at most ~20% CHG-related admixture but in fact about ~25% "ANE".

I have no idea why this is (if it's true) or if there seriously was ANE-related ancestry in South Asia that predated even the arrival of Neolithic West Asians but if this admixture is quite legitimate; there's something even more complex than simply being Australo-Melanesian and Andamanese-related in "ASI".

13 comments:

  1. My models seem to suggest that Proto-Indo-Iranians and Indo-Aryans were more Steppe_EMBA than Steppe_MLBA, but doesn't doesn't mean they didn't come from the Andronovo horizon, from which we only have 3 usable samples.

    Another possibility, albeit less likely one in the context of historical linguistics and archeology, is that they were Catacomb people and basically identical to Yamnaya, thus purely Steppe_EMBA.

    My models also suggest that early Iranians were more Steppe_MLBA than Steppe_EMBA, and may in fact have been identical to Srubnaya people, who are commonly seen as proto-Iranian.

    I don't have any personal preferences in this context. Proto-Indo-Iranians might have been Steppe_EMBA, Steppe_MLBA, or a mix of both. I'd say a mix of both in varying degrees is probably most likely.

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    1. "I don't have any personal preferences in this context. Proto-Indo-Iranians might have been Steppe_EMBA, Steppe_MLBA, or a mix of both. I'd say a mix of both in varying degrees is probably most likely."

      Yes, I considered this possibility myself and while I somewhat doubt it; you maybe onto something here indeed. We'll definitely have things be more clear with more ancient DNA rolling in.

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  2. A minor correction to the Western Asia map you use. That map should have included the Asian part of Egypt in Western Asia and excluded the European part of Turkey from it. This is not just a geographical matter because Balkan Turks are clearly genetically closer to other Balkan peoples than they are to Anatolian Turks (I have seen many Balkan Turkish genetic results to make comparisons) and they genetically cluster with other Balkan peoples rather than with Anatolian Turks, and I suspect Near Eastern Egyptians would genetically cluster with most other Near Eastern Arabs rather than with North African Egyptians if they had been investigated.

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    1. Sure, but I was basically just using the "official" map for West Asia and not really one stringently based on genetics. But I agree that "Balkan Turkey" should be counted out and the Sinai Peninsula should probably be counted in. I haven't seen many Sinai Egyptian results though, other than the results of a few "Bedouin" from the region who did actually seem more Southern-Levantine~Arabian-like than "North African Egyptian", if I recall correctly.

      Thanks for the comment, Onur. :-)

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    2. Yes, but even the "official" definitions of West Asia vary and many of the ones I have seen include the Asian part of Egypt and exclude the European part of Turkey as in this one:

      https://upload.wikimedia.org/wikipedia/commons/d/d3/Western_Asia.png

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    3. Yes, that looks like a better map. I might start using it from now on. And, yes all of these "official" mappings vary. Various definitions of "South Asia" don't include Afghanistan, for example. I was surprised the one I used for this post did include it, actually. I often prefer a term like "South-Central Asia" for Greater Khorasan+Pakistan, to be honest.

      https://drive.google.com/file/d/0B2ARnUeK-Y8WdkV0X2Jzb2Z1aUk/view?usp=sharing

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    4. Actually I prefer a definition of Greater Khorasan excluding Mawarannahr (Transoxiana) and Khwarezm. I think Afghanistan and northern Pakistan can be included in South-Central Asia in genetic studies at least.

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    5. Hmm, I somewhat see your point there (excluding Transoxiana). Now... Just curious... How would you personally divide up South Asia (based on genetics)?

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    6. Hard question. Due to the smoothness of the genetic transition between Iranics and Indo-Aryans, I think geography and languages should be taken more into account than genetics when defining the boundary between South Asia and South-Central Asia. Thus the Indo-Aryan regions of Pakistan should better be included within South Asia, leaving the Iranic regions in South-Central Asia. Don't forget, the boundary between South-Central Asia and Central Asia is today purely politically defined, so don't expect consistency in every regional definition.

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  3. Very interesting Sheikh!! It seems the ANI part of South Asians is a lot more complicated than what is originally thought!!

    What I find astonishing is that now Baloch,Brahui and Makrani seem to have quite substantial Steppe_EMBA (Yamnaya-related if I understand correctly) ancestry now based on the figure above. Which to me I found it contradicting to what I learn from other members including Davidski that Baloch, Brahui and Makrani have very little to none Steppe ancestry.

    But now it seems even they have Steppe/Steppe-related ancestry in significant amounts?

    Hmm cause a bit of intrigued feeling for me. So even South Indians, Maldivians and Sri Lankans should have some Steppe ancestry as well?

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    1. "Very interesting Sheikh!! It seems the ANI part of South Asians is a lot more complicated than what is originally thought!!"

      Thanks for taking interest, my friend. :-) And indeed, lots of folks just saw "ANI" as some single/"pure" cluster when the concept just came out but it's clearly a composite rather than wholly some Caucasus-related cluster (though much of it is actually describable in that way).

      "What I find astonishing is that now Baloch,Brahui and Makrani seem to have quite substantial Steppe_EMBA (Yamnaya-related if I understand correctly) ancestry now based on the figure above. Which to me I found it contradicting to what I learn from other members including Davidski that Baloch, Brahui and Makrani have very little to none Steppe ancestry."

      Very good point and that is one reason why I emboldened the "perhaps" there. Balochis, Makranis and Brahuis are indeed usually very low on Bronze Age steppe ancestry so any estimate showing them with that much MIGHT be rather suspect, to be honest. The only ADMIXTURE run I've seen that created a straight-up Sintashta cluster would be this old one of Kurd's:

      https://docs.google.com/spreadsheets/d/1HazqhPt_EpHrwgjUMNogQvg6vCtf7QkZqiBsb5mWMN8/edit?usp=sharing

      I didn't share these results initially because the run, in my humble opinion, seems a bit messy in some respects but it is interesting in that you get somewhat similar 5-25% estimates for all of the populations in that chart I made but this time Balochis, Makranis and Brahuis have very little "Sintasta-Steppe-Herder" related admixture (1-3%) which might be more in line with the truth.

      "Hmm cause a bit of intrigued feeling for me. So even South Indians, Maldivians and Sri Lankans should have some Steppe ancestry as well?"

      Hmm, I'd say all of these populations probably have just a bit of steppe admixture that mainly shows in their Y-DNA frequencies (i.e. the presence of R1a):

      http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0050269

      https://en.wikipedia.org/wiki/Y-DNA_haplogroups_in_South_Asian_populations

      Though I'm not familiar with the Y-DNA situation in the Maldives. But, overall, I'd say there's probably very little steppe admixture in these groups. I'd be surprised at anything over 1-5%. Though, I think David managed to make estimates over that (I think at just north of 10%? I'd have to double-check to be sure) via using Yamnaya-like samples (one of the reasons why I'm skeptical toward using such steppe herders as their admixture source). But yeah... I'd say groups like Tamils are overwhelmingly "Iran_N-like + ASI" in ancestry. They're much more indicative of some of South Asia's genetic diversity prior to the steppe expansions, from what I've noticed.

      Nevertheless, sufficient ancient DNA from South and Central Asia should clarify things in due time and you can bet I'll do a post (or posts) on that when the time comes. :-)


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  4. Hehe no prob. I think the ANI is diverse as well. Mostly Caucasus or Iran N-like+ Steppe/Steppe-like.


    Hmm only N. and E. Euros score very high Sintashta. For Asians, Pamiris have the most with high amounts in other C. and N. South Asians like Gujarat A, B, Punjabi Sikhs. If this is the case, is the Sintashta and other Steppe admix overestimated by many members? Interesting to ponder.


    Not discrediting any geneticists, is it possible that the model by Lazaridis for high Steppe EMBA/Yamnaya-like admix in the region including Baloch, Brahui, Makrani aren’t accurate? Maybe for them, it is something archaic Indo-European admix that is Steppe-like.


    Notice your second embolden. :-D The 2nd model is very distinct from the 1st by Lazaridis. Baloch, Brahui, Makrani still have substantial Sintashta-related admix. Or is the admix in the three pops representing some archaic Indo-European admix similar to Steppe?


    Can you share the estimates by David to measure admixture in these pops?


    If remember correctly, pops like Tamils, Malayalis are 40-50% W. Eurasian. There were lots of interactions btw S. Indians and SE Asians in trade, religion and culture, and likely lot of intermarriages, absorption of S. Indians into SE Asian society. This [URL="https://en.wikipedia.org/wiki/Mahathir_Mohamad#cite_note-5]former Malaysian PM [/URL] is said to be 1/2 or 1/4 Indian through his father. Another ex. is Raja Sri Lumay, half Tamil half Malay prince from Sumatra who found[URL="https://en.wikipedia.org/wiki/Rajahnate_of_Cebu]Cebu Rajahnate in precolonial Philippines.[/URL]


    A lot of SE Asians who have S. Indian contact like Thais, Malays, Indonesians like Acehnese, Bataks, Cambodians, Burmese should have some Iran-N like West Eurasian admix. In Iran N. K6, Cambodians score [[URL="http://www.anthrogenica.com/showthread.php?8166-Updated-Neolithic-Iranian-Calculator&p=176871&viewfull=1#post176871"]7% West Eurasian (Iran N+ Natufian)[/URL] while in ANE K6, they score [URL="https://docs.google.com/spreadsheets/d/13O_IYAv4SE8jLO9FKOQ5RiHf4vQeOQbSRWa-KsN7wO4/edit#gid=1957523915"]6.3% West Eurasian[/URL] (ANE+Natufian, I think the Iran N/Iran-N like is mostly represented by ANE, Natufian). Here are the [URL="https://docs.google.com/spreadsheets/d/1PWAi-sPU3KniSxgJg-L7CjcXK2K7CXvIrFr8_F-ZhOE/edit#gid=1108042089]full spreadsheets for both calcs. [/URL] *Unfortunately Cambodians are the only SE Asians here but I think they can give an idea of what other SE Asians will score in terms of W. Eurasian ancestry.

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  5. OMG, I thought doing the URL function will work. I will post the links and rewrite some stuff again so you can fully understand my reply. :P

    Here is the link to the former PM of Malaysia that I read is said to be half or 1/4 Indian: https://en.wikipedia.org/wiki/Mahathir_Mohamad

    Here is the info about Rajahnate of Cebu in precolonial Philippines that is said to be found by Sri Lumay, a half Tamil half Malay prince from Sumatra: https://en.wikipedia.org/wiki/Rajahnate_of_Cebu

    A lot of SE Asians who have S. Indian contact like Thais, Malays, Indonesians like Acehnese, Bataks, Cambodians, Burmese should have some Iran-N like West Eurasian admix. In Iran N. K6, Cambodians score 7% West Eurasian (Iran N+ Natufian): http://www.anthrogenica.com/showthread.php?8166-Updated-Neolithic-Iranian-Calculator&p=176871&viewfull=1#post176871
    while in ANE K6, they score 6.3% West Eurasian(ANE+Natufian, I think the Iran N/Iran-N like is mostly represented by ANE, Natufian- https://docs.google.com/spreadsheets/d/13O_IYAv4SE8jLO9FKOQ5RiHf4vQeOQbSRWa-KsN7wO4/edit#gid=1957523915

    Here are the full spreadsheets for both calcs: https://docs.google.com/spreadsheets/d/1PWAi-sPU3KniSxgJg-L7CjcXK2K7CXvIrFr8_F-ZhOE/edit#gid=1108042089

    *Unfortunately Cambodians are the only SE Asians here but I think they can give an idea of what other SE Asians will score in terms of W. Eurasian ancestry.

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